Topics

1

General Questions and Answers / Nedged Elastic Band method

« on: April 5, 2010, 10:03 »

Hi,

I'm asking regarding the NEB method.  I tried modifying the code from the tutorial to apply the NEB method to a bulk material to understand some phase transition issue.  However, I keep getting force=nan error.  I've narrowed it down to the codes in NEB.py when it tried to get the tangent between images which gives a nan value.  As I'm not sure of how to get the tangent, or what it means, so I don't know how to change to code to make it works.

Any suggestions are greatly appreciated.  Thanks in advance.

============
Note: I've modified the code NEB.py and somehow it works.

Change the line:
        utangent=tangent/length(tangent)

To:
        if max(tangent)-0. < 0.01:
          utangent=tangent
        else:
          utangent=tangent/length(tangent)

============

2

General Questions and Answers / Regarding ISOValues [in particular charge density]

« on: November 25, 2009, 11:22 »

Dear all,

Let me refer to a previous post http://quantumwise.com/forum/index.php?topic=126.0
{I'm starting a new one so as not to hijack others' topic}

I would like to know if I can modify the Bloch state [aka wavefunction, phi] calculated {as a function of energy determined by the quantum number, i.e. band number and k-vector} into the charge density {which will also be a function of energy}.

I'm guessing that this would be different from the electron density calculated since that would be summed over all energy and is also dependent on the electron occupancy.  Or can I get the charge density from electron density and occupancy?

Thank you in advance for any info.

3

General Questions and Answers / Visualization of VNL data

« on: November 23, 2009, 05:48 »

Dear all,

I would like to ask if anyone used other software to visualizing the data (e.g., Electron density) in the VNL files other than VNL?
While the graphics looks great using VNL, I can't seems to maneuver the figures to the correct position.  This is especially difficult when I want to compare the plots of different structures as I can't get to the same viewing angle.

Maybe I'm just a control freak but I would love to be able to control the rotation degrees of the figures.  Any tips on this will be great.

Cheers!

4

General Questions and Answers / Inconsistency in gated two probe method

« on: June 15, 2009, 12:23 »

Dear Dr. Blom,

I would like to bring your attention to an inconsistency I observed in gated two probe method.  This is regarding the setting of the ‘Initial Density Type’ under TwoProbe Algorithm Parameters.

I’ve set the value to ‘InitialDensityType.NeutralAtom’ but in the gated method, it reverts back to ‘InitialDensityType.EquivalentBulk’.  I’m not sure if it is intentional and the physical significant of this parameters.  I guess it would not matter as the results should converge to a similar value.

I’ve attached my codes (2Probe.py) and the output (2Probe.log) for your investigation.

Rgds,
Kai Tak

5

General Questions and Answers / calculateAtomicForce

« on: April 24, 2009, 16:52 »

Hi,

I would like to ask some question about the force calculated between 2 atoms.

I assume it is the electrostatic force between the 2 atoms and as the distance between them decreases, the forces between them increases.  If the atoms are of similar charge, the force is repulsive and it is attractive if the atoms are of different polarity.

Question 1: When the force is non-zero and of different polarity, does it mean that if I leave the two atoms be, they will move towards each other? (and hence decreasing the distance between them and increasing the attractive force between them).  This would be true even if the force is small (0.05eV/Ang?).

Question 2: Can I interpret the force as such that it is the force required to increase the distance between the atoms?

Any help is greatly appreciated.

Rgds
Dick

6

General Questions and Answers / Transmission spectrum for GatedTwoProbeMethod

« on: March 13, 2009, 10:14 »

Hi,

I'm having some problem understanding the transmission spectrum for GatedTwoProbe calculations.
I was expecting the transmission to be shifted along the energy axis by the same amount of bias that is applied but that doesn't seem to be the case.  Does defining the screening atoms have any effect on the transmission spectrum?

Rgds,
Dick

7

General Questions and Answers / Issue with parallel two probe calculations

« on: January 28, 2009, 04:26 »

Hi all,

I would like to know if anyone observed that during the calculation of parallel two probe calculation, the SCF loop for the scattering region (The one right after the calculation of Fermi energy of electrodes and before the calculation of charge of the system) runs on a single processor?

I'm just wondering if there is anyway to make that part of the calculation run on the multi-processor to speed things up.

Any suggestions will be much appreciated.

Cheers!
Dick LAM